//
// Manta - Structural Variant and Indel Caller
// Copyright (c) 2013-2019 Illumina, Inc.
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.
//
//

#pragma once

#include "common/Program.hpp"
#include "options/AlignmentFileOptions.hpp"

struct TestAssemblerOptions {
  AlignmentFileOptions alignFileOpt;

  std::string referenceFilename;
  std::string outputFilename;
};

void parseTestAssemblerOptions(
    const illumina::Program& prog, int argc, char* argv[], TestAssemblerOptions& opt);
